The heat treatment process plays a pivotal role in enhancing the characteristics of nickel-based single crystal (NBSC) superalloys. Nevertheless, there exists a paucity of comprehensive investigations concerning the microstructural evolution of NBSC superalloys during heat treatment. This study employs a molecular dynamics simulation method to control the temperature of the NBSC superalloy precisely, aiming to unveil intricate details regarding microstructural evolution, temperature distribution patterns, mechanical properties, and other pertinent aspects during the cooling phase. Additionally, a comparative analysis of internal defect evolution under varying cooling rates is undertaken. The findings highlight the consistently heightened activity of atoms in the γ phase compared to those in the γ' phase. Notably, the stability disparity between these phases gradually diminishes as the temperature decreases during the cooling process. At elevated temperatures, the prevalence of amorphous phases and dislocations in the γ phase channel diminishes concomitantly with the temperature reduction. Strain distribution in the alloy primarily concentrates in the γ phase channel and the central cross position of the γ' phase. The temperature reduction correlates with a decline in the alloy model's strain. In the initial phase of strain reduction, stress fluctuation trends in the X, Y, and Z directions exhibit an initial increase followed by a gradual decrease. Furthermore, the atomic number of HCP defects and dislocation density exhibit distinct patterns of change contingent upon the cooling rates employed.